Thank you but I succeed to make model with one ligand but water molecules are not coming in model but putting second single '.' 

On Thu, Jan 10, 2013 at 7:17 PM, Modeller Caretaker <> wrote:
On 01/10/2013 01:14 AM, Krupal Jethava wrote:
   I am trying to make model with Ligand (37 HetAtom) and 3 water
molecule. I used the same script as in manual but getting the error that
"Number of residue in alignment and pdb are different: 324      288 for
alignment entry: tseq.pdb"

We can't tell for sure without seeing your real input files, but by saying "FIRST:@:END  ::@" (I think you mean "FIRST:@:END  :@:") you are asking Modeller to read all residues from the first chain in the PDB file. So if the ligand and water residues are in a different chain, Modeller won't read them. (Rather than END:@, you could use the residue number and chain ID of the last ligand/water.) Note also that you'll need to set and

        Ben Webb, Modeller Caretaker
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